I am removing my transmission and when I went to take the shifter itself off I ran into a problem. As the picture shows there is a pin. It seems to me that this pin should be hammered through with a punch all the way out the other side. It does not do it. It goes only so far and then will come back the other way but never very far. Do I just need to keep pounding away? Is there something I am missing? Can you drill it out and replace the pin?

 

I'm sure you could drill it out. I would try prying it out first with a good pair of side cutting pliers

 

A manual I have shows those as the cap retainers, don't hit or drill.
Press down on shift lever and rotate retainer CCW then lift lever out.
It looks like a spring below keeps pressure up on the retainer to keep it locked to those two pins, they do not go all the way through , just like a couple of headed dowels pressed in from the inside out.

 

I followed your advice and pushed down and turned ccw. It worked. It took two of us to get it done. Thank you so much!